Variant report

Variant	rs4924410
Chromosome Location	chr15:40339494-40339495
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40337530..40340162-chr15:40384154..40386428,2	MCF-7	breast:
2	chr15:40336254..40340864-chr15:40394731..40398446,8	MCF-7	breast:
3	chr15:40331646..40335428-chr15:40336590..40339827,4	K562	blood:
4	chr15:40338671..40341082-chr15:40391017..40392708,2	MCF-7	breast:
5	chr15:40337354..40339667-chr15:40397161..40399729,4	MCF-7	breast:
6	chr15:40337627..40341020-chr15:40341608..40343639,3	K562	blood:
7	chr15:40336937..40340971-chr15:40343981..40345656,3	K562	blood:
8	chr15:40338929..40343184-chr15:40345688..40348186,4	MCF-7	breast:
9	chr15:40338471..40341053-chr15:40396995..40399108,2	K562	blood:
10	chr15:40335189..40340116-chr15:40397333..40401366,6	K562	blood:
11	chr15:40339113..40341248-chr15:40387682..40389325,2	MCF-7	breast:
12	chr15:40337344..40339688-chr15:40344036..40346311,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000104081	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010879	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070250	0.87[EUR][1000 genomes]
rs11631442	0.83[ASN][1000 genomes]
rs12899649	1.00[CHB][hapmap]
rs12912442	1.00[CHB][hapmap]
rs16924528	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17722502	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17722526	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17723133	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2412456	1.00[CHB][hapmap]
rs2412478	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28444847	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28515996	0.83[ASN][1000 genomes]
rs28736699	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28826672	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35781999	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3923235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4497657	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924417	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62004114	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62004158	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71132133	0.83[ASN][1000 genomes]
rs7181230	0.87[CEU][hapmap]
rs7183977	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs72731415	0.83[ASN][1000 genomes]
rs7497289	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749748	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8026641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937213	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9919974	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9972424	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Ewing sarcoma	22327514	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4924410	EIF2AK4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40332000-40339800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:40336200-40343400	Enhancers	Fetal Heart	heart
3	chr15:40336600-40340600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:40336600-40341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:40336600-40341000	Enhancers	HSMMtube	muscle
6	chr15:40336600-40341200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:40336600-40341800	Enhancers	Fetal Thymus	thymus
8	chr15:40336600-40342800	Enhancers	Spleen	Spleen
9	chr15:40336600-40343000	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:40336800-40341000	Enhancers	Fetal Stomach	stomach
11	chr15:40336800-40341600	Enhancers	Placenta	Placenta
12	chr15:40336800-40342800	Enhancers	Primary B cells from cord blood	blood
13	chr15:40336800-40343400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:40337000-40340400	Enhancers	Stomach Mucosa	stomach
15	chr15:40337000-40340800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:40337000-40340800	Enhancers	Fetal Lung	lung
17	chr15:40337000-40340800	Enhancers	HMEC	breast
18	chr15:40337000-40340800	Enhancers	HUVEC	blood vessel
19	chr15:40337000-40340800	Enhancers	NHLF	lung
20	chr15:40337000-40342200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr15:40337000-40344800	Enhancers	Primary T cells fromperipheralblood	blood
22	chr15:40337400-40340200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:40337400-40342600	Enhancers	Primary hematopoietic stem cells	blood
24	chr15:40337400-40342600	Enhancers	Adipose Nuclei	Adipose
25	chr15:40337400-40343600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr15:40337600-40340400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:40337600-40341000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:40337600-40341000	Enhancers	HSMM	muscle
29	chr15:40337600-40341200	Enhancers	Fetal Muscle Trunk	muscle
30	chr15:40337600-40342800	Weak transcription	Fetal Brain Male	brain
31	chr15:40337800-40339800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:40337800-40340000	Weak transcription	Brain Anterior Caudate	brain
33	chr15:40337800-40340000	Enhancers	Duodenum Mucosa	Duodenum
34	chr15:40337800-40340400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:40337800-40340400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:40337800-40340600	Genic enhancers	Fetal Intestine Small	intestine
37	chr15:40337800-40340600	Enhancers	A549	lung
38	chr15:40337800-40340600	Enhancers	NHDF-Ad	bronchial
39	chr15:40337800-40340800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr15:40337800-40340800	Enhancers	Small Intestine	intestine
41	chr15:40337800-40341000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:40337800-40341400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:40337800-40343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:40337800-40343000	Enhancers	Left Ventricle	heart
45	chr15:40337800-40355600	Weak transcription	Brain Angular Gyrus	brain
46	chr15:40337800-40355600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:40338000-40339600	Weak transcription	Brain Germinal Matrix	brain
48	chr15:40338000-40340000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:40338000-40340600	Weak transcription	Brain Substantia Nigra	brain
50	chr15:40338000-40340800	Enhancers	NH-A	brain

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